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- PDB-1fb5: LOW RESOLUTION STRUCTURE OF OVINE ORNITHINE TRANSCARBMOYLASE IN T... -

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Basic information

Entry
Database: PDB / ID: 1fb5
TitleLOW RESOLUTION STRUCTURE OF OVINE ORNITHINE TRANSCARBMOYLASE IN THE UNLIGANDED STATE
ComponentsORNITHINE TRANSCARBAMOYLASE
KeywordsTRANSFERASE / cooperativity / T-state / ornithine
Function / homology
Function and homology information


response to biotin / L-ornithine catabolic process / monoatomic anion homeostasis / ammonium homeostasis / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / midgut development / Urea cycle / citrulline biosynthetic process / L-arginine biosynthetic process via ornithine ...response to biotin / L-ornithine catabolic process / monoatomic anion homeostasis / ammonium homeostasis / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / midgut development / Urea cycle / citrulline biosynthetic process / L-arginine biosynthetic process via ornithine / urea cycle / Mitochondrial protein import / L-arginine biosynthetic process / response to zinc ion / amino acid binding / phosphate ion binding / liver development / response to insulin / phospholipid binding / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / mitochondrion / identical protein binding
Similarity search - Function
Ornithine/putrescine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold ...Ornithine/putrescine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NORVALINE / Ornithine transcarbamylase, mitochondrial / Ornithine transcarbamylase, mitochondrial
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsZanotti, G. / Battistutta, R. / Panzalorto, M. / Francescato, P. / Bruno, G. / De Gregorio, A.
Citation
Journal: Org.Biomol.Chem. / Year: 2003
Title: Functional and structural characterization of ovine ornithine transcarbamoylase.
Authors: De Gregorio, A. / Battistutta, R. / Arena, N. / Panzalorto, M. / Francescato, P. / Valentini, G. / Bruno, G. / Zanotti, G.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: 1.85 A Resolution Crystal Structure of Human Ornithine Transcarbamoylase Complexed with N-phopshonacetyl-L-ornithine. Catalytic Mechanism and Correlation with Inherited Deficiency.
Authors: Shi, D. / Morizono, H. / Ha, Y. / Aoyagi, M. / Tuchman, M. / Allewell, N.M.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Substrate-induced Conformational Change in a Trimeric Ornithine Transcarbamoylase
Authors: Ha, Y. / McCann, M.T. / Tuchman, M. / Allewell, N.M.
History
DepositionJul 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORNITHINE TRANSCARBAMOYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0052
Polymers35,8881
Non-polymers1171
Water543
1
A: ORNITHINE TRANSCARBAMOYLASE
hetero molecules

A: ORNITHINE TRANSCARBAMOYLASE
hetero molecules

A: ORNITHINE TRANSCARBAMOYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0166
Polymers107,6653
Non-polymers3513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5430 Å2
ΔGint-34 kcal/mol
Surface area37060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)184.700, 184.700, 184.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
DetailsThe biological assembly is a trimer constructed by three identical polypeptyde chains, related by a crystallographic three-forld axis. L-norvaline is positioned in an hypothetical site, in an electron density that could represent a protein side chain.

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Components

#1: Protein ORNITHINE TRANSCARBAMOYLASE / OTCASE


Mass: 35888.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: LIVER
References: UniProt: P00480, UniProt: P84010*PLUS, ornithine carbamoyltransferase
#2: Chemical ChemComp-NVA / NORVALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2 / Details: Synthesized
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ACTIVE SITE CAVITY IS EMPTY AND THE PROTEIN CAN BE CONSIDERED TO BE IN THE T STATE.
Nonpolymer detailsL-NORVALINE IS POSITIONED IN A HYPOTHETICAL SITE, IN AN ELECTRON DENSITY THAT COULD REPRESENT A ...L-NORVALINE IS POSITIONED IN A HYPOTHETICAL SITE, IN AN ELECTRON DENSITY THAT COULD REPRESENT A PROTEIN SIDE CHAIN.
Sequence detailsTHE AUTHORS USED THE HUMAN AMINO ACID SEQUENCE, SINCE THE OVINE ONE WAS NOT AVAILABLE. ASP IS ...THE AUTHORS USED THE HUMAN AMINO ACID SEQUENCE, SINCE THE OVINE ONE WAS NOT AVAILABLE. ASP IS PRESENT AT 297 IN DATABASE REFERENCE. SHI ET AL., J.BIOL.CHEM 1998, 273:34347-24254 LISTS ALA AT 297.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 7.32 Å3/Da / Density % sol: 83.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 8% PEG 4000, 0.1 M Na acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298.K
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17-9 mg/mlprotein1drop
210 mMTris-HCl1reservoirpH7.4
30.1 Msodium acetate1reservoir
48 %(w/v)PEG40001reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 3.5→500 Å / Num. obs: 13959 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 48.7 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.3
Reflection shellResolution: 3.51→3.92 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.32 / Num. unique all: 3877 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementResolution: 3.5→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The human amino acid sequence was used, since the ovine one was not available
RfactorNum. reflection% reflectionSelection details
Rfree0.252 674 -random, I>3sigma(I)
Rwork0.212 ---
all0.219 13375 --
obs0.219 13375 95.3 %-
Refinement stepCycle: LAST / Resolution: 3.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2503 0 8 3 2514
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.92
Refinement
*PLUS
Rfactor Rfree: 0.25 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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